ArticleGigaScience2022
Allele-specific regulatory effects on the pig transcriptome.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 13 citations in OpenAlex.
- The influence of structural variants from 2445 pigs on gene expression and complex traits.Nature communications · 2026Article
- Mapping the landscape of allele-specific expression in porcine genomes.Genome biology · 2026Article
- A scalable framework for single-cell eQTL mapping uncovers genetic regulators of meat production traits in pigs.Journal of animal science and biotechnology · 2026Article
- Single-nucleus transcriptome profiling of skeletal muscle in Diqing Tibetan pigs with distinct body sizes.BMC genomics · 2025Article
- The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed.Genetics, selection, evolution : GSE · 2025Article
- A New Family-Based Approach for Detecting Allele-Specific Expression and for Mapping Possible eQTLs.Animals : an open access journal from MDPI · 2025Article
- Cell-cell communication-mediated cell-type-specific parent-of-origin effects in mammals.Nature communications · 2025Article
- Short Communication: The imprinted and paternally expressed MIMT1 lncRNA ortholog in pigs.Journal of animal science · 2025Article
- Multi-omic characterization of allele-specific regulatory variation in hybrid pigs.Nature communications · 2024Article
- Allele-specific regulatory effects on the pig transcriptome.GigaScience · 2022Article
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAllele-specific expression (ASE) refers to the preferential expression of one allele over the other and contributes to adaptive phenotypic plasticity. Here, we used a reciprocal cross-model between phenotypically divergent European Berkshire and Asian Tibetan pigs to characterize 2 ASE classes: imprinting (i.e., the unequal expression between parental alleles) and sequence dependent (i.e., unequal expression between breed-specific alleles). We examined 3 transcript types, including protein-coding genes (PCGs), long noncoding RNAs, and transcripts of unknown coding potential, across 7 representative somatic tissues from hybrid pigs generated by reciprocal crosses.
resultsWe identified a total of 92 putative imprinted transcripts, 69 (75.00%) of which are described here for the first time. By combining the transcriptome from purebred Berkshire and Tibetan pigs, we found ∼6.59% of PCGs are differentially expressed between breeds that are regulated by trans-elements (e.g., transcriptional factors), while only ∼1.35% are attributable to cis (e.g., promoters). The higher prevalence of trans-PCGs indicates the dominated effects of trans-regulation in driving expression differences and shaping adaptive phenotypic plasticity between breeds, which were supported by functional enrichment analysis. We also found strong evidence that expression changes mediated by cis-effects were associated with accumulated variants in promoters.
conclusionsOur study provides a comprehensive map of expression regulation that constitutes a valuable resource for the agricultural improvement of pig breeds.
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